- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x YD1: 6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione(Non-covalent)
YD1.1: 16 residues within 4Å:- Chain A: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, M.165, E.166, H.172, D.187, R.188, Q.189
12 PLIP interactions:11 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:H.41, A:Q.189
- Hydrogen bonds: A:G.143, A:S.144, A:S.144, A:E.166
- Water bridges: A:N.142, A:N.142, A:C.145, B:S.1
- pi-Stacking: A:H.41
- Halogen bonds: A:D.187
YD1.2: 16 residues within 4Å:- Chain B: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, M.165, E.166, H.172, D.187, R.188, Q.189
13 PLIP interactions:12 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:H.41, B:Q.189
- Hydrogen bonds: B:G.143, B:S.144, B:S.144, B:E.166, B:E.166
- Water bridges: B:N.142, B:N.142, B:C.145, A:S.1
- pi-Stacking: B:H.41
- Halogen bonds: B:D.187
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Clyde, A. et al., High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J.Chem.Inf.Model. (2022)
- Release Date
- 2021-03-03
- Peptides
- 3C-like proteinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
SMTL ID : 7ltj.1
Room-temperature X-ray structure of SARS-CoV-2 main protease (3CL Mpro) in complex with a non-covalent inhibitor Mcule-5948770040
3C-like proteinase
Toggle Identical (AB)Related Entries With Identical Sequence
5r7y.1 | 5r7z.1 | 5r80.1 | 5r81.1 | 5r82.1 | 5r83.1 | 5r84.1 | 5r8t.1 | 5re4.1 | 5re5.1 | 5re6.1 | 5re7.1 | 5re8.1 | 5re9.1 | 5rea.1 | 5reb.1 | 5rec.1 | 5red.1 | 5ree.1 | 5ref.1 | 5reg.1 | 5reh.1 | 5rei.1 | 5rej.1 | 5rek.1 | 5rel.1 | 5rem.1 | 5ren.1 | 5reo.1 | 5rep.1 more...less...5rer.1 | 5res.1 | 5ret.1 | 5reu.1 | 5rev.1 | 5rew.1 | 5rex.1 | 5rey.1 | 5rez.1 | 5rf0.1 | 5rf1.1 | 5rf2.1 | 5rf3.1 | 5rf4.1 | 5rf5.1 | 5rf6.1 | 5rf7.1 | 5rf8.1 | 5rf9.1 | 5rfa.1 | 5rfb.1 | 5rfc.1 | 5rfd.1 | 5rfe.1 | 5rff.1 | 5rfg.1 | 5rfh.1 | 5rfi.1 | 5rfj.1 | 5rfk.1 | 5rfl.1 | 5rfm.1 | 5rfn.1 | 5rfo.1 | 5rfp.1 | 5rfq.1 | 5rfr.1 | 5rfs.1 | 5rft.1 | 5rfu.1 | 5rfv.1 | 5rfw.1 | 5rfx.1 | 5rfy.1 | 5rfz.1 | 5rg0.1 | 5rg1.1 | 5rg2.1 | 5rg3.1 | 5rgg.1 | 5rgh.1 | 5rgi.1 | 5rgj.1 | 5rgk.1 | 5rgl.1 | 5rgm.1 | 5rgn.1 | 5rgo.1 | 5rgp.1 | 5rgq.1 | 5rgr.1 | 5rgs.1 | 5rgt.1 | 5rgu.1 | 5rgv.1 | 5rgw.1 | 5rgx.1 | 5rgy.1 | 5rgz.1 | 5rh0.1 | 5rh1.1 | 5rh2.1 | 5rh3.1 | 5rh4.1 | 5rh5.1 | 5rh6.1 | 5rh7.1 | 5rh8.1 | 5rh9.1 | 5rha.1 | 5rhb.1 | 5rhc.1 | 5rhd.1 | 5rhe.1 | 5rhf.1 | 5rl0.1 | 5rl1.1 | 5rl2.1 | 5rl3.1 | 5rl4.1 | 5rl5.1 | 5sml.1 | 5smm.1 | 5smn.1 | 6lu7.1 | 6m03.1 | 6m2n.1 | 6m2n.2 | 6m2q.1 | 6w63.1 | 6wnp.1 | 6wqf.1 | 6wtj.1 | 6wtk.1 | 6wtm.1 | 6xb0.1 | 6xb1.1 | 6xb2.1 | 6xch.1 | 6xhm.1 | 6xhu.1 | 6xkf.1 | 6xkh.1 | 6xqs.1 | 6xqt.1 | 6xqu.1 | 6xr3.1 | 6y2e.1 | 6y2f.1 | 6y84.1 | 6ynq.1 | 6yvf.1 | 6z2e.1 | 6zrt.1 | 6zru.1 | 7a1u.1 | 7abu.1 | 7adw.1 | 7af0.1 | 7aga.1 | 7aha.1 | 7ak4.1 | 7aku.1 | 7alh.1 | 7ali.1 | 7amj.1 | 7ans.1 | 7ap6.1 | 7aph.1 | 7aqe.1 | 7aqi.1 | 7aqj.1 | 7ar5.1 | 7ar6.1 | 7arf.1 | 7au4.1 | 7avd.1 | 7awr.1 | 7aws.1 | 7awu.1 | 7aww.1 | 7ax6.1 | 7axm.1 | 7axo.1 | 7ay7.1 | 7b2j.1 | 7b2u.1 | 7b3e.1 | 7b5z.1 | 7b77.1 | 7baj.1 | 7bak.1 | 7bal.1 | 7bb2.1 | 7be7.1 | 7bfb.1 | 7bgp.1 | 7bij.1 | 7bqy.1 | 7buy.1 | 7c6s.1 | 7c6u.1 | 7c7p.1 | 7c8b.1 | 7c8r.1 | 7c8t.1 | 7c8u.1 | 7com.1 | 7cut.1 | 7cuu.1 | 7cwb.1 | 7cx9.1 | 7d1o.1 | 7d3i.1 | 7d64.1 | 7dat.1 | 7dau.1 | 7dav.1 | 7dgb.1 | 7dgf.1 | 7dgg.1 | 7dgh.1 | 7dgi.1 | 7dhj.1 | 7djr.1 | 7dk1.1 | 7dpu.1 | 7dpv.1 | 7dpv.2 | 7e18.1 | 7e19.1 | 7e5x.1 | 7ein.1 | 7en8.1 | 7en9.1 | 7fay.1 | 7faz.1 | 7gav.1 | 7gaw.1 | 7gax.1 | 7gay.1 | 7gaz.1 | 7gb0.1 | 7gb1.1 | 7gb2.1 | 7gb3.1 | 7gb4.1 | 7gb5.1 | 7gb6.1 | 7gb7.1 | 7gb8.1 | 7gb9.1 | 7gba.1 | 7gbb.1 | 7gbc.1 | 7gbd.1 | 7gbe.1 | 7gbf.1 | 7gbg.1 | 7gbh.1 | 7gbi.1 | 7gbj.1 | 7gbk.1 | 7gbl.1 | 7gbm.1 | 7gbn.1 | 7gbo.1 | 7gbp.1 | 7gbq.1 | 7gbr.1 | 7gbs.1 | 7gbt.1 | 7gbu.1 | 7gbv.1 | 7gbw.1 | 7gbx.1 | 7gby.1 | 7gbz.1 | 7gc0.1 | 7gc1.1 | 7gc2.1 | 7gc3.1 | 7gc4.1 | 7gc5.1 | 7gc6.1 | 7gc7.1 | 7gc8.1 | 7gc9.1 | 7gca.1 | 7gcb.1 | 7gcc.1 | 7gcd.1 | 7gce.1 | 7gcf.1 | 7gcg.1 | 7gci.1 | 7gcj.1 | 7gck.1 | 7gcl.1 | 7gcm.1 | 7gcn.1 | 7gco.1 | 7gcp.1 | 7gcq.1 | 7gcr.1 | 7gcs.1 | 7gct.1 | 7gcu.1 | 7gcv.1 | 7gcw.1 | 7gcx.1 | 7gcy.1 | 7gcz.1 | 7gd0.1 | 7gd1.1 | 7gd2.1 | 7gd3.1 | 7gd4.1 | 7gd5.1 | 7gd6.1 | 7gd7.1 | 7gd8.1 | 7gd9.1 | 7gda.1 | 7gdb.1 | 7gdc.1 | 7gdd.1 | 7gde.1 | 7gdf.1 | 7gdg.1 | 7gdh.1 | 7gdi.1 | 7gdj.1 | 7gdk.1 | 7gdl.1 | 7gdm.1 | 7gdn.1 | 7gdo.1 | 7gdp.1 | 7gdq.1 | 7gdr.1 | 7gds.1 | 7gdt.1 | 7gdu.1 | 7gdv.1 | 7gdw.1 | 7gdx.1 | 7gdy.1 | 7gdz.1 | 7ge0.1 | 7ge1.1 | 7ge2.1 | 7ge3.1 | 7ge4.1 | 7ge5.1 | 7ge6.1 | 7ge7.1 | 7ge8.1 | 7ge9.1 | 7gea.1 | 7geb.1 | 7gec.1 | 7ged.1 | 7gee.1 | 7gef.1 | 7geg.1 | 7geh.1 | 7gei.1 | 7gej.1 | 7gek.1 | 7gel.1 | 7gem.1 | 7gen.1 | 7geo.1 | 7geq.1 | 7ger.1 | 7ges.1 | 7get.1 | 7geu.1 | 7gev.1 | 7gew.1 | 7gex.1 | 7gey.1 | 7gez.1 | 7gf0.1 | 7gf1.1 | 7gf2.1 | 7gf3.1 | 7gf4.1 | 7gf5.1 | 7gf6.1 | 7gf7.1 | 7gf8.1 | 7gf9.1 | 7gfa.1 | 7gfb.1 | 7gfc.1 | 7gfd.1 | 7gfe.1 | 7gff.1 | 7gfg.1 | 7gfh.1 | 7gfi.1 | 7gfj.1 | 7gfk.1 | 7gfl.1 | 7gfm.1 | 7gfn.1 | 7gfo.1 | 7gfp.1 | 7gfq.1 | 7gfr.1 | 7gfs.1 | 7gft.1 | 7gfu.1 | 7gfv.1 | 7gfw.1 | 7gfx.1 | 7gfy.1 | 7gfz.1 | 7gg0.1 | 7gg1.1 | 7gg2.1 | 7gg3.1 | 7gg4.1 | 7gg5.1 | 7gg6.1 | 7gg7.1 | 7gg8.1 | 7gg9.1 | 7gga.1 | 7ggb.1 | 7ggc.1 | 7ggd.1 | 7gge.1 | 7ggf.1 | 7ggg.1 | 7ggh.1 | 7ggi.1 | 7ggj.1 | 7ggk.1 | 7ggl.1 | 7ggm.1 | 7ggn.1 | 7ggo.1 | 7ggp.1 | 7ggq.1 | 7ggr.1 | 7ggs.1 | 7ggt.1 | 7ggu.1 | 7ggv.1 | 7ggw.1 | 7ggx.1 | 7ggy.1 | 7ggz.1 | 7gh0.1 | 7gh1.1 | 7gh2.1 | 7gh3.1 | 7gh4.1 | 7gh5.1 | 7gh6.1 | 7gh7.1 | 7gh8.1 | 7gh9.1 | 7gha.1 | 7ghb.1 | 7ghc.1 | 7ghd.1 | 7ghe.1 | 7ghf.1 | 7ghg.1 | 7ghh.1 | 7ghi.1 | 7ghj.1 | 7ghk.1 | 7ghl.1 | 7ghm.1 | 7ghn.1 | 7gho.1 | 7ghp.1 | 7ghq.1 | 7ghr.1 | 7ghs.1 | 7ght.1 | 7ghu.1 | 7ghv.1 | 7ghw.1 | 7ghx.1 | 7ghy.1 | 7ghz.1 | 7gi0.1 | 7gi1.1 | 7gi2.1 | 7gi3.1 | 7gi4.1 | 7gi5.1 | 7gi6.1 | 7gi7.1 | 7gi8.1 | 7gi9.1 | 7gia.1 | 7gib.1 | 7gic.1 | 7gid.1 | 7gie.1 | 7gif.1 | 7gig.1 | 7gih.1 | 7gii.1 | 7gij.1 | 7gik.1 | 7gil.1 | 7gim.1 | 7gin.1 | 7gio.1 | 7gip.1 | 7giq.1 | 7gir.1 | 7gis.1 | 7git.1 | 7giu.1 | 7giv.1 | 7giw.1 | 7gix.1 | 7giy.1 | 7giz.1 | 7gj0.1 | 7gj1.1 | 7gj2.1 | 7gj3.1 | 7gj4.1 | 7gj5.1 | 7gj6.1 | 7gj7.1 | 7gj8.1 | 7gj9.1 | 7gja.1 | 7gjb.1 | 7gjc.1 | 7gjd.1 | 7gje.1 | 7gjf.1 | 7gjg.1 | 7gjh.1 | 7gji.1 | 7gjj.1 | 7gjk.1 | 7gjl.1 | 7gjm.1 | 7gjn.1 | 7gjo.1 | 7gjp.1 | 7gjq.1 | 7gjr.1 | 7gjs.1 | 7gjt.1 | 7gju.1 | 7gjv.1 | 7gjw.1 | 7gjx.1 | 7gjy.1 | 7gjz.1 | 7gk0.1 | 7gk1.1 | 7gk2.1 | 7gk3.1 | 7gk4.1 | 7gk5.1 | 7gk6.1 | 7gk7.1 | 7gk8.1 | 7gk9.1 | 7gka.1 | 7gkb.1 | 7gkc.1 | 7gkd.1 | 7gke.1 | 7gkf.1 | 7gkg.1 | 7gkh.1 | 7gki.1 | 7gkj.1 | 7gkk.1 | 7gkl.1 | 7gkm.1 | 7gkn.1 | 7gko.1 | 7gkp.1 | 7gkq.1 | 7gkr.1 | 7gks.1 | 7gkt.1 | 7gku.1 | 7gkv.1 | 7gkw.1 | 7gkx.1 | 7gky.1 | 7gkz.1 | 7gl0.1 | 7gl1.1 | 7gl2.1 | 7gl3.1 | 7gl4.1 | 7gl5.1 | 7gl6.1 | 7gl7.1 | 7gl8.1 | 7gl9.1 | 7gla.1 | 7glb.1 | 7glc.1 | 7gld.1 | 7gle.1 | 7glf.1 | 7glg.1 | 7glh.1 | 7gli.1 | 7glj.1 | 7glk.1 | 7gll.1 | 7glm.1 | 7gln.1 | 7glo.1 | 7glp.1 | 7glq.1 | 7glr.1 | 7gls.1 | 7glt.1 | 7glu.1 | 7glv.1 | 7glw.1 | 7glx.1 | 7gly.1 | 7glz.1 | 7gm0.1 | 7gm1.1 | 7gm2.1 | 7gm3.1 | 7gm4.1 | 7gm5.1 | 7gm6.1 | 7gm7.1 | 7gm8.1 | 7gm9.1 | 7gma.1 | 7gmb.1 | 7gmc.1 | 7gmd.1 | 7gme.1 | 7gmf.1 | 7gmg.1 | 7gmh.1 | 7gmi.1 | 7gmj.1 | 7gmk.1 | 7gml.1 | 7gmm.1 | 7gmn.1 | 7gmo.1 | 7gmp.1 | 7gmq.1 | 7gmr.1 | 7gms.1 | 7gmt.1 | 7gmu.1 | 7gmv.1 | 7gmw.1 | 7gmx.1 | 7gmy.1 | 7gmz.1 | 7gn0.1 | 7gn1.1 | 7gn2.1 | 7gn3.1 | 7gn4.1 | 7gn5.1 | 7gn6.1 | 7gn7.1 | 7gn8.1 | 7gn9.1 | 7gna.1 | 7gnb.1 | 7gnc.1 | 7gnd.1 | 7gne.1 | 7gnf.1 | 7gng.1 | 7gnh.1 | 7gni.1 | 7gnj.1 | 7gnk.1 | 7gnl.1 | 7gnm.1 | 7gnn.1 | 7gno.1 | 7gnp.1 | 7gnq.1 | 7gnr.1 | 7gns.1 | 7gnt.1 | 7gnu.1 | 7gre.1 | 7grf.1 | 7grg.1 | 7grh.1 | 7gri.1 | 7grj.1 | 7grk.1 | 7grl.1 | 7grm.1 | 7grn.1 | 7gro.1 | 7grp.1 | 7grq.1 | 7grr.1 | 7grs.1 | 7grt.1 | 7gru.1 | 7grv.1 | 7grw.1 | 7grx.1 | 7gry.1 | 7grz.1 | 7gs0.1 | 7gs1.1 | 7gs2.1 | 7gs3.1 | 7gs4.1 | 7gs5.1 | 7gs6.1 | 7jfq.1 | 7jp0.1 | 7jp1.1 | 7jpy.1 | 7jpz.1 | 7jq0.1 | 7jq1.1 | 7jq2.1 | 7jq3.1 | 7jq4.1 | 7jq5.1 | 7jr3.1 | 7jr4.1 | 7jst.1 | 7jsu.1 | 7jt0.1 | 7jt7.1 | 7ju7.1 | 7jun.1 | 7jvz.1 | 7jw8.1 | 7jw8.2 | 7jyc.1 | 7k3t.1 | 7k40.1 | 7k6d.1 | 7k6e.1 | 7khp.1 | 7kph.1 | 7kx5.1 | 7kyu.1 | 7l0d.1 | 7l10.1 | 7l11.1 | 7l12.1 | 7l13.1 | 7l14.1 | 7l5d.1 | 7l8i.1 | 7l8j.1 | 7lb7.1 | 7lbn.1 | 7lco.1 | 7lcr.1 | 7lcs.1 | 7lct.1 | 7ldl.1 | 7lkd.1 | 7lke.1 | 7lmd.1 | 7lme.1 | 7lmf.1 | 7ltn.1 | 7lyh.1 | 7m2p.1 | 7m8m.1 | 7m8n.1 | 7m8o.1 | 7m8p.1 | 7m8x.1 | 7m8y.1 | 7m8z.1 | 7m90.1 | 7m91.1 | 7mat.1 | 7mau.1 | 7mav.1 | 7maw.1 | 7max.1 | 7maz.1 | 7mb0.1 | 7mb1.1 | 7mb2.1 | 7mb3.1 | 7mb3.2 | 7mb3.3 | 7mbg.1 | 7mbi.1 | 7mbi.2 | 7mhf.1 | 7mhg.1 | 7mhh.1 | 7mhi.1 | 7mhj.1 | 7mhk.1 | 7mhl.1 | 7mhm.1 | 7mhn.1 | 7mho.1 | 7mhp.1 | 7mhq.1 | 7mlg.1 | 7mng.1 | 7mrr.1 | 7n44.1 | 7n8c.1 | 7nbr.1 | 7nbs.1 | 7nbt.1 | 7nby.1 | 7neo.1 | 7nev.1 | 7nf5.1 | 7ng3.1 | 7ng6.1 | 7nij.1 | 7nt1.1 | 7nt2.1 | 7nt3.1 | 7ntq.1 | 7nts.1 | 7ntt.1 | 7ntv.1 | 7ntw.1 | 7nuk.1 | 7nw2.1 | 7nwx.1 | 7nxh.1 | 7o46.1 | 7p2g.1 | 7p35.1 | 7p51.1 | 7pfl.1 | 7pfm.1 | 7phz.1 | 7pxz.1 | 7pzq.1 | 7q5e.1 | 7q5f.1 | 7qbb.1 | 7qka.1 | 7qt8.1 | 7r7h.1 | 7rbz.1 | 7rc0.1 | 7rfr.1 | 7rfs.1 | 7rfu.1 | 7rls.1 | 7rm2.1 | 7rmb.1 | 7rme.1 | 7rmt.1 | 7rmz.1 | 7rn0.1 | 7rn1.1 | 7rn4.1 | 7rnh.1 | 7rnk.1 | 7rnw.1 | 7rnw.2 | 7rvn.1 | 7rvq.1 | 7rvs.1 | 7rvx.1 | 7s3k.1 | 7s3s.1 | 7s4b.1 | 7s6w.1 | 7set.1 | 7sf1.1 | 7sf3.1 | 7sfb.1 | 7sfh.1 | 7sfi.1 | 7sgh.1 | 7sgh.2 | 7sh7.1 | 7sh8.1 | 7sh9.1 | 7si9.1 | 7t2t.1 | 7tdu.1 | 7te0.1 | 7teh.1 | 7tek.1 | 7tel.1 | 7tfr.1 | 7tia.1 | 7tiu.1 | 7tiv.1 | 7tiw.1 | 7tix.1 | 7tiy.1 | 7tiz.1 | 7tj0.1 | 7tuu.1 | 7u92.1 | 7ukk.1 | 7ur9.1 | 7uu6.1 | 7uu7.1 | 7uu8.1 | 7uu9.1 | 7uub.1 | 7uuc.1 | 7uud.1 | 7uue.1 | 7v1t.1 | 7v7m.1 | 7vfa.1 | 7vfb.1 | 7vh8.1 | 7vic.1 | 7vjw.1 | 7vjx.1 | 7vjy.1 | 7vjz.1 | 7vk0.1 | 7vk1.1 | 7vk2.1 | 7vk3.1 | 7vk4.1 | 7vk5.1 | 7vk6.1 | 7vk7.1 | 7vk8.1 | 7vvt.1 | 7wo1.1 | 7wo2.1 | 7wo3.1 | 7wof.1 | 7wym.1 | 7wyp.1 | 7x6j.1 | 7x6k.1 | 7xar.1 | 7z2k.1 | 7z2k.2 | 7z3u.1 | 7z4s.1 | 7zqv.1 | 7zv5.1 | 7zv7.1 | 7zv8.1 | 8a4q.1 | 8acd.1 | 8acl.1 | 8aeb.1 | 8aiq.1 | 8aiv.1 | 8aiz.1 | 8b56.1 | 8b56.2 | 8bfq.1 | 8bga.1 | 8bgd.1 | 8bs1.1 | 8bs2.1 | 8cdc.1 | 8cyu.1 | 8cyu.2 | 8cyz.1 | 8cyz.2 | 8cz4.1 | 8cz4.2 | 8cz7.1 | 8cz7.2 | 8d4p.1 | 8dib.1 | 8dic.1 | 8did.1 | 8die.1 | 8dif.1 | 8dig.1 | 8dih.1 | 8dii.1 | 8dl9.1 | 8dlb.1 | 8dmd.1 | 8dsu.1 | 8dz0.1 | 8dz2.1 | 8dzb.1 | 8dzc.1 | 8eoy.1 | 8ezv.1 | 8ezz.1 | 8f02.1 | 8f2c.1 | 8f2d.1 | 8fiv.1 | 8fiw.1 | 8ftc.1 | 8ftl.1 | 8fy6.1 | 8fy7.1 | 8gtv.1 | 8gtw.1 | 8gvd.1 | 8gvy.1 | 8gxg.1 | 8gxh.1 | 8gxi.1 | 8gzb.1 | 8hbk.1 | 8hht.1 | 8hi9.1 | 8htv.1 | 8i30.1 | 8ifp.1 | 8ifq.1 | 8ifr.1 | 8ifs.1 | 8ift.1 | 8ign.1 | 8igo.1 | 8igx.1 | 8igy.1 | 8jop.1 | 8okb.1 | 8okc.1 | 8okk.1 | 8okl.1 | 8okm.1 | 8okn.1 | 8ph4.1 | 8q71.1 | 8q71.2 | 8r11.1 | 8r12.1 | 8r14.1 | 8r16.1 | 8s9z.1 | 8sk4.1 | 8skh.1 | 8sty.1 | 8stz.1 | 8sxr.1 | 8tbe.1 | 8tpd.1 | 8uab.1 | 8uh5.1 | 8uho.1 | 8uia.1 | 8uif.1 | 8ups.1 | 8upv.1 | 8upw.1 | 8ute.1 | 8vsg.1